Document Detail


Electronic properties of the amino acid side chains contribute to the structural preferences in protein folding.
MedLine Citation:
PMID:  11444376     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
A database of 118 non-redundant proteins was examined to determine the preferences of amino acids for secondary structures: alpha-helix, beta-strand and coil conformations. To better understand how the physicochemical properties of amino acid side chains might influence protein folding, several new scales have been suggested for quantifying the electronic effects of amino acids. These include the pKa at the amino group, localized effect substituent constants (esigma), and a composite of these two scales (epsilon). Amino acids were also classified into 5 categories on the basis of their electronic properties: O (strong electron donor), U (weak donor), Z (ambivalent), B (weak electron acceptor), and X (strong acceptor). Certain categories of amino acid appeared to be critical for particular conformations, e.g., O and U-type residues for alpha-helix formation. Pairwise analysis of the database according to these categories revealed significant context effects in the structural preferences. In general, the propensity of an amino acid for a particular conformation was related to the electronic features of the side chain. Linear regression analyses revealed that the electronic properties of amino acids contributed about as much to the folding preferences as hydrophobicity, which is a well-established determinant of protein folding. A theoretical model has been proposed to explain how the electronic properties of the side chain groups might influence folding along the peptide backbone.
Authors:
D S Dwyer
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Publication Detail:
Type:  Journal Article    
Journal Detail:
Title:  Journal of biomolecular structure & dynamics     Volume:  18     ISSN:  0739-1102     ISO Abbreviation:  J. Biomol. Struct. Dyn.     Publication Date:  2001 Jun 
Date Detail:
Created Date:  2001-07-10     Completed Date:  2001-12-26     Revised Date:  2008-11-21    
Medline Journal Info:
Nlm Unique ID:  8404176     Medline TA:  J Biomol Struct Dyn     Country:  United States    
Other Details:
Languages:  eng     Pagination:  881-92     Citation Subset:  IM    
Affiliation:
Department of Psychiatry, LSU Health Sciences Center-Shreveport, 71130-3932, USA. ddwyer@lsuhsc.edu
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MeSH Terms
Descriptor/Qualifier:
Amino Acid Motifs
Amino Acid Sequence
Amino Acids / chemistry*
Chemistry, Physical
Databases, Protein
Hydrophobicity
Kinetics
Models, Chemical
Physicochemical Phenomena
Protein Conformation*
Protein Folding*
Static Electricity
Chemical
Reg. No./Substance:
0/Amino Acids

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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